Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions
Abstract
:1. Introduction
2. Results
2.1. Performances of Eight Lines under K-Concentration Gradients
2.2. Phenotypic Variations of Root Traits in the Association Panel under Low-K Stress
2.3. QTL Clusters Related to the Root System under Low-K Stress Were Obtained by GWAS
2.4. Candidate Genes Associated with Root-Related Traits
2.5. GO and KEGG Analysis of Potential Candidate Genes
2.6. Protein Interaction Network Analysis, Phylogenetic Trees, Gene Structure Analysis, and Motif Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Experimental Design and Growth Condition
4.3. Root Phenotyping
4.4. Data Analysis
4.5. Marker–Trait Association
4.6. Exploration of Candidate Genes
4.7. GO and KEGG Analysis
4.8. Protein Interaction Network Analysis, Phylogenetic Trees, Gene-Structure Analysis, and Motif Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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Classification | Trait Description | Abbreviations | Units |
---|---|---|---|
Root-related traits | Primary root length | PRL | cm |
Total root volume | TRV | cm3 | |
Total root surface area | TSA | cm2 | |
Total root length | TRL | cm | |
Total root number | TRN | N | |
Biomass-related traits | Root fresh weight | RFW | g |
Shoot fresh weight | SFW | g | |
Total fresh weights | TFW | g | |
Root–shoot fresh weight ratio | RSR |
Trait | Mean | SD | Min | Max | Skewness | Kurtosis | CV (%) | H2 (%) |
---|---|---|---|---|---|---|---|---|
PRL | 23.57 | 2.77 | 13.72 | 31.62 | −0.05 | 0.35 | 11.73 | 56.9 |
SFW | 2.47 | 0.44 | 1.20 | 3.72 | 0.01 | −0.07 | 17.83 | 60.4 |
RFW | 0.43 | 0.08 | 0.23 | 0.71 | 0.28 | 0.65 | 18.38 | 60.3 |
TRL | 711.5 | 115.1 | 409.8 | 1156.3 | 0.47 | 1.16 | 16.17 | 53.1 |
TSA | 51.7 | 8.54 | 30.2 | 87.4 | 0.42 | 0.94 | 16.51 | 52.6 |
TRV | 0.31 | 0.06 | 0.14 | 0.53 | 0.29 | 0.17 | 19.15 | 49.4 |
TRN | 1084.1 | 310.5 | 540.3 | 3417.2 | 2.22 | 11.39 | 28.64 | 52.1 |
TFW | 2.90 | 0.49 | 1.43 | 4.35 | −0.01 | −0.12 | 17.03 | 60.2 |
RSR | 0.18 | 0.03 | 0.09 | 0.31 | 0.89 | 1.54 | 18.27 | 62.1 |
Cluster | Trait | Lead SNP | Position (bp) | Gene Model | Distance to Lead SNP (Kb) | Gene Symbol | At Homolog Genes | Annotation |
---|---|---|---|---|---|---|---|---|
qRT.A02-4 | RFW, RSR | Bn-A02-p13803435 | 10,432,009 | BnaA02g17300D | −29.99 | SAUR | AT1G75580 | SAUR-like auxin-responsive protein family |
qRT.A02-11 | TRN, RSR | Bn-A02-p8199891 | 5,191,339 | BnaA02g10340D | −94.04 | CRF3 | AT5G53290 | Cytokinin response factor 3 |
qRT.A03-12 | TSA, TRV, RSR | Bn-A03-p10023639 | 9,214,456 | BnaA03g19500D | −22.93 | CKX1 | AT2G41510 | Cytokinin oxidase/dehydrogenase 1 |
qRT.A03-17 | TRL, TSA | seq-new-rs32620 | 2,981,029 | BnaA03g06500D | 76.26 | UGP2 | AT5G17310 | UDP-glucose pyrophosphorylase 2 |
BnaA03g06730D | −35.11 | MYB56 | AT5G17800 | MYB domain protein 56 | ||||
BnaA03g06800D | −61.10 | SAUR | AT5G18010 | SAUR-like auxin-responsive protein family | ||||
qRT.A04-4 | RSR, TRL, TSA, TRV | Bn-A04-p12314909 | 13,306,243 | BnaA04g16140D | 97.43 | GH3 | AT1G48670 | Auxin-responsive GH3 family protein |
qRT.A05-11 | TSA, TRV | Bn-A05-p2142102 | 2,273,504 | BnaA05g04380D | −85.25 | ERF13 | AT2G44840 | Ethylene-responsive element binding factor 13 |
qRT.A06-10 | RSR, TRN | seq-new-rs33430 | 2,265,805 | BnaA06g03580D | 71.58 | GH3 | AT1G23160 | Auxin-responsive GH3 family protein |
BnaA06g03620D | 33.41 | RACK1B_AT | AT1G48630 | Receptor for activated C kinase 1B | ||||
qRT.A07-1 | PRL, RSR | Bn-A07-p21573107 | 23,110,821 | BnaA07g33740D | 25.48 | ARF17 | AT1G77850 | Auxin response factor 17 |
qRT.A07-6 | TRV, RSR | seq-new-rs40608 | 9,704,794 | BnaA07g10150D | 25.95 | PIN7 | AT1G23080 | PIN-FORMED 7 |
qRT.A08-1 | RSR, SFW | seq-new-rs39127 | 12,905,937 | BnaA08g15590D | −35.17 | CP1 | AT4G36880 | Cysteine proteinase1 |
BnaA08g15600D | −56.19 | GASA1 | AT1G75750 | GAST1 protein homolog 1 | ||||
qRT.A09-4 | TFW, SFW | seq-new-rs26492 | 25,679,360 | BnaA09g35190D | 21.94 | SDIR1 | AT3G55530 | SALT- AND DROUGHT-INDUCED RING FINGER1 |
BnaA09g35230D | −3.72 | P5CS2 | AT3G55610 | Delta 1-pyrroline-5-carboxylate synthase 2 | ||||
qRT.A10-1 | SFW, TFW | Bn-A10-p15967013 | 15,593,735 | BnaA10g23640D | 16.74 | GA20OX3 | AT5G07200 | Gibberellin 20-oxidase 3 |
BnaA10g23650D | 9.42 | RR21 | AT5G07210 | Response regulator 21 | ||||
BnaA10g23740D | −42.10 | ML4 | AT5G07290 | MEI2-like 4 | ||||
qRT.A10-3 | RSR, RFW | Bn-A10-p10120142 | 11,533,850 | BnaA10g14470D | 28.88 | EIL2 | AT5G21120 | ETHYLENE-INSENSITIVE3-like 2 |
qRT.C01-7 | RSR, TRV, RFW | seq-new-rs38417 | 12,806,484 | BnaC01g18450D | −24.27 | LTI65 | AT5G52300 | LOW-TEMPERATURE-INDUCED 65 |
qRT.C04-2 | SFW, TFW | Bn-scaff_16888_1-p1169101 | 45,355,403 | BnaC04g45700D | 33.58 | AUX1 | AT2G38120 | AUXIN RESISTANT 1 |
BnaC04g45720D | 23.19 | CAX1 | AT2G38170 | Cation exchanger 1 | ||||
BnaC04g45770D | −11.70 | AT2G38240 | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein | |||||
qRT.C04-8 | RSR, TRV | seq-new-rs30573 | 25,264,080 | BnaC04g24310D | −42.70 | EIF3E | AT3G57290 | Eukaryotic translation initiation factor 3E |
qRT.C06-10 | TRV, RSR | seq-new-rs48045 | 5,209,723 | BnaC06g04590D | −14.14 | AT1G51460 | ABC-2 type transporter family protein | |
BnaC06g04620D | −63.33 | AT1G51538 | Aminotransferase-like, plant mobile domain family protein | |||||
qRT.C07-1 | TRV, TRN | seq-new-rs28637 | 44,197,394 | BnaC07g46640D | 28.74 | LCR59 | AT4G30070 | Low-molecular-weight cysteine-rich 59 |
qRT.C07-2 | RSR, TRL | seq-new-rs46639 | 35,175,730 | BnaC07g30830D | 55.17 | LR | AT5G23400 | Leucine-rich repeat (LRR) family protein |
BnaC07g30930D | −19.94 | SAR1 | AT1G33410 | SUPPRESSOR OF AUXIN RESISTANCE1 | ||||
qRT.C07-6 | TRL, TSA, TRV | Bn-scaff_18202_1-p1536412 | 22,287,865 | BnaC07g16350D | −20.37 | ABA1 | AT5G67030 | ABA DEFICIENT 1 |
qRT.C08-5 | RSR, SFW | seq-new-rs34390 | 29,522,206 | BnaC08g29060D | 64.89 | AFB3 | AT1G12820 | Auxin signaling F-box 3 |
BnaC08g29120D | 41.24 | LBD29 | AT3G58190 | Lateral organ boundaries-domain 29 | ||||
qRT.C09-1 | TRV, RSR | seq-new-rs41567 | 42,567,030 | BnaC09g40100D | −55.68 | WOX12 | AT5G17810 | WUSCHEL related homeobox 12 |
qRT.C09-2 | RFW, RSR | seq-new-rs25004 | 38,586,454 | BnaC09g35190D | −14.05 | AT5G59845 | Gibberellin-regulated family protein |
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Ibrahim, S.; Ahmad, N.; Kuang, L.; Tian, Z.; Sadau, S.B.; Iqbal, M.S.; Wang, X.; Wang, H.; Dun, X. Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions. Plants 2022, 11, 1826. https://doi.org/10.3390/plants11141826
Ibrahim S, Ahmad N, Kuang L, Tian Z, Sadau SB, Iqbal MS, Wang X, Wang H, Dun X. Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions. Plants. 2022; 11(14):1826. https://doi.org/10.3390/plants11141826
Chicago/Turabian StyleIbrahim, Sani, Nazir Ahmad, Lieqiong Kuang, Ze Tian, Salisu Bello Sadau, Muhammad Shahid Iqbal, Xinfa Wang, Hanzhong Wang, and Xiaoling Dun. 2022. "Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions" Plants 11, no. 14: 1826. https://doi.org/10.3390/plants11141826